Scatter the squash and onions on a rimmed baking sheet, drizzle with the olive oil and season with 1/2 teaspoon salt. Toss well to coat evenly.
Roast until the squash is tender all the way through and the onions are soft and turning golden brown, 28 to 30 minutes. Let cool slightly.
Unroll the pie crust onto a nonstick baking sheet. Crumble half of the cheese over the crust, leaving a 2-inch border. Top with the roasted onions and then shingle with the squash in circles. Fold the crust borders up and over the filling, crimping every 2 inches or so. Sprinkle the exposed squash with the pistachios and the remaining cheese.
Bake until the crust is golden brown and the cheese is melted, about 30 minutes. Let cool for 5 minutes, then sprinkle with the arugula and pomegranate seeds.